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IconHeatmap_Viz.R
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IconHeatmap_Viz.R
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#install(gplots)
require(gplots)
#install(RColorBrewer)
require(RColorBrewer)
#install.packages("Cairo")
require(Cairo)
#####"iconheatmap_viz" uses the "icon_list_getter" function defined in main catscan R script.
#####BEGIN user input information#####
#Must define a string for variable "path"
#Must have a folder named "zip" in your directory where the zip files are located
#Define the iconheatmap_viz function first, then run the function with the path to the directory as the only input (line 208)
#Must define a string for variable "newNameOrder_path" to the location of the csv that holds the icon order desired for heatmap outputs
#Define the iconheatmap_viz_newNameOrder function first, then run the function with the 'path' to the directory, and newNameOrder_path as the only inputs (line 402)
#Line 199 (393 for newNameOrder) contains Legend creation for the heatmaps. Comment out if not desired
path <- 'C:/Users...'
newNameOrder_path <- "C:/Users/.../newNameOrder.csv"
#####END user input#####
iconheatmap_viz <- function(path){
##Checks if "/" exists after path. If not, one is added
if(substr(path, nchar(path), nchar(path)) != "/"){
path <- paste(path, "/", sep = "")
}
##Creates a folder "icon" within the path to save the icon names csv to
klipart_path <- paste(path, "icon/", sep = "")
dir.create(klipart_path)
##Creates a folder "heatmaps" within the path to save the heatmap images to
heatmap_path <- paste(path, "heatmaps/", sep = "")
dir.create(heatmap_path)
##Creates a folder "unzipped" within the path to save the unzipped folders to
unzipped_path <- paste(path, "unzipped/", sep = "")
dir.create(unzipped_path)
##Icon list getter: get a list of icon names
##It also saves the icon.csv needed for KlipArt
icon_list_getter <- function(path){
#Construct the zip folder path and list all the zip files
zip_path <- paste(path, "zip/", sep = "")
files <- list.files(zip_path)
#Sets the working directory to the unzipped folder
setwd(unzipped_path)
#Unzip the zip file from the 1st participant
first_p <- unzip(paste(zip_path, files[1], sep = ""))
#Sets the working directory to the unzipped folder
setwd(unzipped_path)
#Get the participant number for the first participant
first_p_number <- substring(files[1], 1, nchar(files[1]) - 4)
#Construct the full file name for icons.csv
icons_csv <- paste("./", first_p_number, "/", first_p_number, "icons.csv", sep = "")
#Read in icons.csv
icons <- read.csv(icons_csv, header = F, stringsAsFactors = F)
#Reorder icon names by icon index
icons <- icons[order(icons[, 1]),]
#Extract the icon names from the table (excluding the path name and file extensions)
icon_list <- icons[, 2]
for(i in 1:length(icon_list)){
end <- regexpr("\\.[^\\.]*$", icon_list[i])[1]
icon_list[i] <- substr(icon_list[i], 9, end - 1)
}
#Extract the icon names with file type (e.g. .jpg) for KlipArt
icon_list_klipart <- icons
for(j in 1:nrow(icon_list_klipart)){
icon_list_klipart[j, 2] <- substr(icon_list_klipart[j, 2], 9, nchar(icon_list_klipart[j, 2]))
}
colnames(icon_list_klipart) <- c("index", "icon_names")
#Sort the icon list by index
icon_list_klipart <- icon_list_klipart[order(icon_list_klipart$index) , ]
#Export the list as a csv file
write.table(icon_list_klipart, file = paste(klipart_path, "icon.csv", sep = ""),
sep = ",", row.names = F, col.names = F)
#Return the icon list as a vector
return(icon_list)
}
##Defines variable "all_icons" as a list of icon names
all_icons <- sort(icon_list_getter(path))
#####IconHeatmap_Viz#####
##Read in files
zip_path <- paste(path, "zip/", sep="")
files <- list.files(zip_path)
##Begins for loop to loop through participants' zip folders
for(p in files){
#Sets the working directory to the unzipped folder
setwd(unzipped_path)
##Unzippes participant folder
participant <- unzip(paste(zip_path, p, sep=""))
##Looks for the "assignment.csv" file within the now unzipped folder
check <- participant[6]
if(substr(check, nchar(check) - 13, nchar(check)) != "assignment.csv"){
check <- participant[4]
}
##reads in "assignnmet.csv" file
d <- read.delim(check, header=FALSE, sep=",",stringsAsFactors=F)
d <- d[order(d[,3]),]
##Gathers linguistic responses from participants
batch <- unzip(paste(zip_path, p, sep=""))
check <- batch[6]
if(substr(check, nchar(check) - 13, nchar(check)) != "batch.csv"){
check <- batch[5]
}
##Reads in linguistic response data
batch_file <- read.delim(check, header=FALSE, sep=",",stringsAsFactors=F)
linguistic_info <- batch_file[,2:3]
##outputs the unique integers in column 2 of the csv
groups <- unique(d[,2])
##creates an empty list called "all_groups"
all_groups <- list()
##fills in the created "all_groups" list with the groups the participant created
for(group in groups){
all_groups[[group+1]] <- d[d[,2] == group,]
}
##creates an empty data frame
df <- data.frame()
##matches all integers in specific group to other integers within that group
for(k in 1:length(all_groups)){
for(i in 1:length(all_groups[[k]][,3])){
for(j in 1:length(all_groups[[k]][,3])){
combo <- c(all_groups[[k]][i, 3], all_groups[[k]][j, 3], k-1)
df <- rbind(df, combo)
# print(combo)
}
}
}
####MATRIX####
##creates empty matrix
m <- matrix(data = NA, nrow = nrow(d), ncol = nrow(d))
##fills in matrix from combo values of data frame
for(i in 1:nrow(df)){
x <- df[i, 1]+1
y <- df[i, 2]+1
m[x, y] <- df[i, 3]
}
colnames(m) <- all_icons
rownames(m) <- all_icons
ngroups <- length(groups)
myBreaks <- -1:ngroups
myColors <- c((rgb(102, 194, 165, maxColorValue=255)), (rgb(252, 141, 98, maxColorValue=255)), (rgb(166, 216, 84, maxColorValue=255)), (rgb(228, 26, 28, maxColorValue=255)), (rgb(231, 138, 165, maxColorValue=255)), (rgb(141, 160, 203, maxColorValue=255)), (rgb(55, 126, 184, maxColorValue=255)), (rgb(152, 78, 163, maxColorValue=255)), (rgb(77, 175, 74, maxColorValue=255)), (rgb(255, 127, 0, maxColorValue=255)), (rgb(255, 255, 51, maxColorValue=255)), (rgb(166, 86, 40, maxColorValue=255)), (rgb(229, 196, 148, maxColorValue=255)), (rgb(50, 50, 50, maxColorValue=255)), (rgb(110, 110, 110, maxColorValue=255)), (rgb(170, 170, 170, maxColorValue=255)), (rgb(255, 255, 153, maxColorValue=255)))
myColors <- append(myColors, brewer.pal(12, "Paired"))
myColors <- append(myColors, brewer.pal(11, "Set3"))
myColors <- myColors[(1:(ngroups+1))]
p <- substr(p, 1, nchar(p) - 4 )
jpeg(filename = paste(heatmap_path, p, "heatmap.jpeg", sep = ""),
quality=7000, width = 1200, height = 1200, pointsize = 18)
heatmap.2(m, Rowv = NA, Colv = NA, trace = "none", col = myColors,
breaks = myBreaks, key = "FALSE", na.color = "black")
title(p)
cex=0.2
legend("topleft",legend=(linguistic_info[,2]), fill=myColors)
dev.off()
}
}
#Run the function to create icon heatmaps
iconheatmap_viz(path)
#####################################################################################################################
iconheatmap_viz_newNameOrder <- function(path, newNameOrder_path){
##Checks if "/" exists after path. If not, one is added
if(substr(path, nchar(path), nchar(path)) != "/"){
path <- paste(path, "/", sep = "")
}
# Read in reorder csv that reorgaizes the icon order
newNameOrder <- read.delim(newNameOrder_path, header=FALSE, sep=",")
##Creates a folder "icon" within the path to save the icon names csv to
klipart_path <- paste(path, "icon/", sep = "")
dir.create(klipart_path)
##Creates a folder "heatmaps" within the path to save the heatmap images to
heatmap_path <- paste(path, "heatmaps/", sep = "")
dir.create(heatmap_path)
##Creates a folder "unzipped" within the path to save the unzipped folders to
unzipped_path <- paste(path, "unzipped/", sep = "")
dir.create(unzipped_path)
##Icon list getter: get a list of icon names
##It also saves the icon.csv needed for KlipArt
icon_list_getter <- function(path){
#Construct the zip folder path and list all the zip files
zip_path <- paste(path, "zip/", sep = "")
files <- list.files(zip_path)
#Sets the working directory to the unzipped folder
setwd(unzipped_path)
#Unzip the zip file from the 1st participant
first_p <- unzip(paste(zip_path, files[1], sep = ""))
#Get the participant number for the first participant
first_p_number <- substring(files[1], 1, nchar(files[1]) - 4)
#Construct the full file name for icons.csv
icons_csv <- paste("./", first_p_number, "/", first_p_number, "icons.csv", sep = "")
#Read in icons.csv
icons <- read.csv(icons_csv, header = F, stringsAsFactors = F)
#Reorder icon names by icon index
icons <- icons[order(icons[, 1]),]
#Extract the icon names from the table (excluding the path name and file extensions)
icon_list <- icons[, 2]
for(i in 1:length(icon_list)){
end <- regexpr("\\.[^\\.]*$", icon_list[i])[1]
icon_list[i] <- substr(icon_list[i], 9, end - 1)
}
#Extract the icon names with file type (e.g. .jpg) for KlipArt
icon_list_klipart <- icons
for(j in 1:nrow(icon_list_klipart)){
icon_list_klipart[j, 2] <- substr(icon_list_klipart[j, 2], 9, nchar(icon_list_klipart[j, 2]))
}
colnames(icon_list_klipart) <- c("index", "icon_names")
#Sort the icon list by index
icon_list_klipart <- icon_list_klipart[order(icon_list_klipart$index) , ]
#Export the list as a csv file
write.table(icon_list_klipart, file = paste(klipart_path, "icon.csv", sep = ""),
sep = ",", row.names = F, col.names = F)
#Return the icon list as a vector
return(icon_list)
}
##Defines variable "all_icons" as a list of icon names
all_icons <- sort(icon_list_getter(path))
#####IconHeatmap_Viz#####
##Read in files
zip_path <- paste(path, "zip/", sep="")
files <- list.files(zip_path)
##Begins for loop to loop through participants' zip folders
for(p in files){
#Sets the working directory to the unzipped folder
setwd(unzipped_path)
##Unzippes participant folder
participant <- unzip(paste(zip_path, p, sep=""))
##Looks for the "assignment.csv" file within the now unzipped folder
check <- participant[6]
if(substr(check, nchar(check) - 13, nchar(check)) != "assignment.csv"){
check <- participant[4]
}
##reads in "assignnmet.csv" file
d <- read.delim(check, header=FALSE, sep=",",stringsAsFactors=F)
d <- d[order(d[,3]),]
##Gathers linguistic responses from participants
batch <- unzip(paste(zip_path, p, sep=""))
check <- batch[6]
if(substr(check, nchar(check) - 13, nchar(check)) != "batch.csv"){
check <- batch[5]
}
##Reads in linguistic response data
batch_file <- read.delim(check, header=FALSE, sep=",",stringsAsFactors=F)
linguistic_info <- batch_file[,2:3]
##outputs the unique integers in column 2 of the csv
groups <- unique(d[,2])
##creates an empty list called "all_groups"
all_groups <- list()
##fills in the created "all_groups" list with the groups the participant created
for(group in groups){
all_groups[[group+1]] <- d[d[,2] == group,]
}
##creates an empty data frame
df <- data.frame()
##matches all integers in specific group to other integers within that group
for(k in 1:length(all_groups)){
for(i in 1:length(all_groups[[k]][,3])){
for(j in 1:length(all_groups[[k]][,3])){
combo <- c(all_groups[[k]][i, 3], all_groups[[k]][j, 3], k-1)
df <- rbind(df, combo)
# print(combo)
}
}
}
####MATRIX####
##creates empty matrix
m <- matrix(data = NA, nrow = nrow(d), ncol = nrow(d))
##fills in matrix from combo values of data frame
for(i in 1:nrow(df)){
x <- df[i, 1]+1
y <- df[i, 2]+1
m[x, y] <- df[i, 3]
}
# orginal is colnames and rownames is 'all_icons', this refers to index '3' in line 329
colnames(m) <- all_icons
rownames(m) <- all_icons
## REORDERS THE MATRIX ACCORDING TO ORDER DEFINED IN nerNameOrder
m <- m[newNameOrder[,1],newNameOrder[,1]]
ngroups <- length(groups)
myBreaks <- -1:ngroups
myColors <- c((rgb(102, 194, 165, maxColorValue=255)), (rgb(252, 141, 98, maxColorValue=255)), (rgb(166, 216, 84, maxColorValue=255)), (rgb(228, 26, 28, maxColorValue=255)), (rgb(231, 138, 165, maxColorValue=255)), (rgb(141, 160, 203, maxColorValue=255)), (rgb(55, 126, 184, maxColorValue=255)), (rgb(152, 78, 163, maxColorValue=255)), (rgb(77, 175, 74, maxColorValue=255)), (rgb(255, 127, 0, maxColorValue=255)), (rgb(255, 255, 51, maxColorValue=255)), (rgb(166, 86, 40, maxColorValue=255)), (rgb(229, 196, 148, maxColorValue=255)), (rgb(50, 50, 50, maxColorValue=255)), (rgb(110, 110, 110, maxColorValue=255)), (rgb(170, 170, 170, maxColorValue=255)), (rgb(255, 255, 153, maxColorValue=255)))
myColors <- append(myColors, brewer.pal(12, "Paired"))
myColors <- append(myColors, brewer.pal(11, "Set3"))
myColors <- myColors[(1:(ngroups+1))]
p <- substr(p, 1, nchar(p) - 4 )
jpeg(filename = paste(heatmap_path, p, "heatmap.jpeg", sep = ""),
quality=7000, width = 1200, height = 1200, pointsize = 18)
heatmap.2(m, Rowv = NA, Colv = NA, trace = "none", col = myColors,
breaks = myBreaks, key = "FALSE", na.color = "black")
title(p)
cex=0.2
legend("topleft",legend=(linguistic_info[,2]), fill=myColors)
dev.off()
}
}
#Run the function to create icon heatmaps reordered
iconheatmap_viz_newNameOrder(path, newNameOrder_path)